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Quiz. 3.
1. While studying 2D protein profiles of the serum samples from healthy and high-risk
subjects for of cardiovascular disease a researcher discovers that a protein spot
consistently present in control subjects (healthy) but is absent in the high-risk patients.
He goes ahead to identify this protein, but MALDI analysis of tryptic fragments did not
match with known database. He gets partial amino acid sequence of this protein. What
can you suggest him in terms of the methods and logics that will lead to identification and
characterization of this protein and gene? Presume that it is a novel protein and gene.
2. Following samples of nucleic acids were isolated and their base ratios were calculated
(values are given below).
Sample 1:
A+T/G+C
0.8
A+G/C+T
1.0
Sample 2:
0.5
1.4
Sample 3:
0.6
1.0
a) Which samples are DNA and which are/is RNA?
b) Which sample will have higher melting point?
3. Why is the discovery of the double-stranded helical structure of DNA in 1953 by
Watson and Crick considered to be one of the most important groundbreaking discoveries
of 20th century?
4. List the differences between protein -helix and B-DNA helix.
5. Describe the characteristic features of B-DNA structure.
6. Meselson and Stahl (1958) labeled the DNA of a bacterium by N15 by growing in N15 food source in media. They found that the density of N15 -labeled DNA had higher
density compared to unlabeled DNA and these could be easily resolved on a density
gradient ultra-centrifugation as two distinct bands. When bacteria with fully labeled
DNA were grown in a new media without any N15 for one generation, and DNA was
isolated and resolved on density gradient ultra-centrifugation, the DNA band appeared
exactly half way between the labeled and un-labeled bands observed previously. Explain
the reason behind this observation and importance of this experiment.
N15
Unlabeled
7. What is DNA melting temperature? How is it measured?
8. Absorbance of UV light by DNA is increased when it is denatured. This effect is
called
I. Melting point II. UV Denaturation III. Hyperchromic effect IV. Hypochromic effect
9. Pulsed field gel electrophoresis is used for separation of
I.
Proteins of high molecular weight.
II.
tRNAs and rRNAs
III.
Very large molecules of DNA
IV.
Small DNA molecules
10. The week interaction force called H-bonding between the nitrogenous bases A & T
and G & C is the basis for
I.
The preservation of genetic information
between the two generations.
II.
The transmission of genetic information
from parent cell to daughter cells.
III.
The southern blot hybridization
IV.
DNA Microarray chip analysis and DNA
fingerprinting.
V.
Transfer of genetic information from DNA
to mRNA (transcription)
VI.
Colony hybridization, PCR and structure of
DNA double helix
VII. All of the above
VIII. None of the above
11. Density-gradient ultra-centrifugation is used for the separation of
I.
small protein from plasmid DNA
II.
bacterial DNA from RNA
III.
bacterial plasmid DNA from genomic DNA
IV.
all of the above
12. How can you isolate single stranded DNA from double stranded DNA?
13. What is thermal chromatography?
14. What is the difference between Topoisomerase I and II?
15. Label the bands corresponding to super-coiled, circular and linear forms of a
plasmid DNA separated on agarose gel in the figure below;
16. How can you prove that H-bonding is not responsible for the stabilization of double
helical structure of DNA?
17. Bases of Watson-Crick base pairs (A-T and G-C) have natural tendency to form Hbonding (electronic complementarities), much more than the non-Watson-Crick base
pairs. What kind of experiment was done to prove it?
18. Why does the osmotic pressure adenine decreases with increase in its concentration
whereas that of sodium chloride increases with concentration?
19. Sequencing by Maxam –Gilbert method (chemical sequencing) requires;
I.
Labeling of the 3’-end of the DNA and cleavage of DNA with separate
chemical reactions
II.
Labeling of the 5’-end of DNA followed by DNA polymerase reaction with
separate nucleotides
III.
Labelling of 5’-end of DNA followed by base-specific chemical cleavage of
the DNA
IV.
All of the above
20. Which end of the DNA is labeled in Sanger’s method of sequencing (dideoxy
method)?
21. Deduce the sequence of the DNA based on the following gel picture which was
obtained by running the reaction mixtures from chemical sequencing reactions.
A+G
G
C
C+T
22. You have obtained from a company, a plasmid containing a foreign DNA insert of 1.2
kb corresponding to a known gene. The product specification indicates that the insert
was cloned using Pst-1 and restriction enzyme and the size of the recombinant plasmid is
5.0 kb. What will you do to confirm that you have the correct insert, and that it is the
specific genes you wanted? Indicate the size of the DNA fragments on agarose gel.
23. What is RFLP and how is it useful for diagnostic purpose for genetic disease?
24. What are the enzymes that allow researchers to cut, paste and duplicate specific
pieces of DNA.
25. What makes sticky ends sticky?
26. You were asked to isolate and clone the gene for a novel protein whose partial
sequence is known. The project requires the identification of regulatory sequences i. e.
promoter and starter regions of the genes and well as introns. Write down your strategy
to approach this problem.
27. Suppose you are scientist in-charge of a forensic investigation of a murder case. The
hairs and blood samples were collected from the crime seen. There are two suspects in
custody. Write down step by step instruction to identify the guilty.
28. Suppose the DNA fingerprints of the samples did not match with any suspects but
they matched with the victim. What will be your guess about the case.
29. A comparative proteomic analysis of normal vs cancerous tissue indicated that there
is a shift in the position of a protein spot in cancer tissue, which shifts back to normal
after the treatment. The gene corresponding to this protein was found to be expressed at
the same levels in both samples as indicated by a DNA microarray analysis for
comparative gene expression between the normal and cancerous tissue. What would be
your explanation about the use and role of this protein in cancer development.
30. What is common in all nucleic acids?
31. Draw the chemical structure of adenosine (a ribonucleoside)
32. Draw the chemical structure of all the deoxyribonucleotides.